Starting phenix.real_space_refine on Mon May 12 02:02:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.map" model { file = "/net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wss_37823/05_2025/8wss_37823.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5624 2.51 5 N 1489 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1749 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1720 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 149 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8797 At special positions: 0 Unit cell: (86.52, 122.776, 131.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1617 8.00 N 1489 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 983.0 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.911A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.623A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.108A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.959A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.672A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.656A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.944A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 225 removed outlier: 3.761A pdb=" N ASP H 224 " --> pdb=" O GLU H 221 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 225 " --> pdb=" O ALA H 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 221 through 225' Processing helix chain 'R' and resid 111 through 138 Processing helix chain 'R' and resid 145 through 173 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 181 through 216 removed outlier: 3.806A pdb=" N THR R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU R 187 " --> pdb=" O THR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 222 Processing helix chain 'R' and resid 224 through 250 removed outlier: 4.050A pdb=" N VAL R 228 " --> pdb=" O ARG R 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU R 231 " --> pdb=" O SER R 227 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 272 through 286 removed outlier: 4.262A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 303 Processing helix chain 'R' and resid 313 through 348 removed outlier: 3.675A pdb=" N CYS R 337 " --> pdb=" O VAL R 333 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 338 " --> pdb=" O PHE R 334 " (cutoff:3.500A) Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 349 through 351 No H-bonds generated for 'chain 'R' and resid 349 through 351' Processing helix chain 'R' and resid 357 through 384 Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 392 removed outlier: 3.677A pdb=" N VAL R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.887A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.556A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.965A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.798A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.482A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.580A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.659A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 147 through 149 removed outlier: 3.541A pdb=" N GLU H 247 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP H 177 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 156 through 161 Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AB6, first strand: chain 'R' and resid 253 through 254 433 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2812 1.34 - 1.46: 2220 1.46 - 1.58: 3854 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 8983 Sorted by residual: bond pdb=" N ARG L 11 " pdb=" CA ARG L 11 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.37e-02 5.33e+03 7.13e+00 bond pdb=" N MET R 165 " pdb=" CA MET R 165 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.04e-02 9.25e+03 5.24e+00 bond pdb=" N ASN R 194 " pdb=" CA ASN R 194 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.97e+00 bond pdb=" N SER R 195 " pdb=" CA SER R 195 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.90e+00 bond pdb=" N GLN R 196 " pdb=" CA GLN R 196 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.56e+00 ... (remaining 8978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 11911 1.22 - 2.43: 212 2.43 - 3.65: 49 3.65 - 4.87: 12 4.87 - 6.08: 5 Bond angle restraints: 12189 Sorted by residual: angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" N LEU H 11 " ideal model delta sigma weight residual 114.23 116.73 -2.50 8.80e-01 1.29e+00 8.04e+00 angle pdb=" N THR R 272 " pdb=" CA THR R 272 " pdb=" C THR R 272 " ideal model delta sigma weight residual 113.18 109.75 3.43 1.33e+00 5.65e-01 6.63e+00 angle pdb=" O ASN R 194 " pdb=" C ASN R 194 " pdb=" N SER R 195 " ideal model delta sigma weight residual 122.12 124.64 -2.52 1.06e+00 8.90e-01 5.65e+00 angle pdb=" CA ASN R 194 " pdb=" C ASN R 194 " pdb=" O ASN R 194 " ideal model delta sigma weight residual 120.55 118.05 2.50 1.06e+00 8.90e-01 5.58e+00 angle pdb=" CA GLY H 10 " pdb=" C GLY H 10 " pdb=" O GLY H 10 " ideal model delta sigma weight residual 122.33 120.55 1.78 8.10e-01 1.52e+00 4.80e+00 ... (remaining 12184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 4952 13.91 - 27.82: 242 27.82 - 41.74: 87 41.74 - 55.65: 21 55.65 - 69.56: 2 Dihedral angle restraints: 5304 sinusoidal: 1992 harmonic: 3312 Sorted by residual: dihedral pdb=" CA GLN R 196 " pdb=" CB GLN R 196 " pdb=" CG GLN R 196 " pdb=" CD GLN R 196 " ideal model delta sinusoidal sigma weight residual -180.00 -122.57 -57.43 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N LEU R 284 " pdb=" CA LEU R 284 " pdb=" CB LEU R 284 " pdb=" CG LEU R 284 " ideal model delta sinusoidal sigma weight residual -180.00 -125.25 -54.75 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA LYS G 46 " pdb=" CB LYS G 46 " pdb=" CG LYS G 46 " pdb=" CD LYS G 46 " ideal model delta sinusoidal sigma weight residual -180.00 -125.41 -54.59 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 835 0.024 - 0.049: 318 0.049 - 0.073: 135 0.073 - 0.097: 66 0.097 - 0.121: 51 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA MET R 112 " pdb=" N MET R 112 " pdb=" C MET R 112 " pdb=" CB MET R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 166 " pdb=" N PRO R 166 " pdb=" C PRO R 166 " pdb=" CB PRO R 166 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 1402 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 112 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 113 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 113 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 14 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO L 15 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO G 55 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.015 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 94 2.65 - 3.21: 7892 3.21 - 3.77: 13415 3.77 - 4.34: 18204 4.34 - 4.90: 30790 Nonbonded interactions: 70395 Sorted by model distance: nonbonded pdb=" OD1 ASP A 229 " pdb=" CD1 LEU A 232 " model vdw 2.082 3.460 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.220 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG H 203 " pdb=" OD2 ASP H 224 " model vdw 2.254 3.120 ... (remaining 70390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8986 Z= 0.118 Angle : 0.703 58.956 12195 Z= 0.363 Chirality : 0.038 0.121 1405 Planarity : 0.003 0.049 1532 Dihedral : 9.953 69.560 3157 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.43 % Allowed : 8.53 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1119 helix: 2.57 (0.27), residues: 376 sheet: 1.50 (0.32), residues: 273 loop : -0.85 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.002 0.000 HIS R 179 PHE 0.007 0.001 PHE R 161 TYR 0.010 0.001 TYR R 275 ARG 0.003 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.17554 ( 433) hydrogen bonds : angle 5.48833 ( 1203) SS BOND : bond 0.02631 ( 3) SS BOND : angle 24.10526 ( 6) covalent geometry : bond 0.00191 ( 8983) covalent geometry : angle 0.45624 (12189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7345 (mtm110) REVERT: A 29 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7314 (ttpt) REVERT: A 195 HIS cc_start: 0.7562 (m-70) cc_final: 0.7216 (t70) REVERT: A 252 SER cc_start: 0.8985 (t) cc_final: 0.8691 (m) REVERT: B 79 LEU cc_start: 0.8583 (mp) cc_final: 0.8356 (mt) REVERT: B 239 ASN cc_start: 0.8612 (m-40) cc_final: 0.8336 (m-40) REVERT: H 109 ASP cc_start: 0.8721 (p0) cc_final: 0.8507 (p0) REVERT: H 221 GLU cc_start: 0.7539 (pm20) cc_final: 0.7149 (pt0) REVERT: R 109 ASN cc_start: 0.4767 (p0) cc_final: 0.4100 (m-40) REVERT: R 127 ASN cc_start: 0.5928 (m-40) cc_final: 0.5721 (m-40) REVERT: R 198 THR cc_start: 0.8398 (t) cc_final: 0.8173 (m) REVERT: R 202 ILE cc_start: 0.8040 (mm) cc_final: 0.7795 (mt) REVERT: R 261 VAL cc_start: 0.7207 (m) cc_final: 0.6815 (p) REVERT: R 280 TYR cc_start: 0.6684 (t80) cc_final: 0.6441 (t80) outliers start: 4 outliers final: 1 residues processed: 247 average time/residue: 0.2232 time to fit residues: 73.3025 Evaluate side-chains 142 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN A 304 GLN B 183 HIS B 220 GLN B 230 ASN H 39 GLN H 143 GLN H 184 GLN R 281 GLN R 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121536 restraints weight = 10973.935| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.81 r_work: 0.3272 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8986 Z= 0.126 Angle : 0.530 6.307 12195 Z= 0.279 Chirality : 0.042 0.157 1405 Planarity : 0.004 0.047 1532 Dihedral : 3.721 37.678 1231 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.30 % Allowed : 11.30 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1119 helix: 2.65 (0.27), residues: 377 sheet: 1.47 (0.32), residues: 252 loop : -0.99 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.008 0.001 HIS R 170 PHE 0.024 0.001 PHE R 286 TYR 0.012 0.001 TYR R 275 ARG 0.005 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 433) hydrogen bonds : angle 4.22409 ( 1203) SS BOND : bond 0.01336 ( 3) SS BOND : angle 2.48045 ( 6) covalent geometry : bond 0.00273 ( 8983) covalent geometry : angle 0.52713 (12189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.997 Fit side-chains REVERT: A 24 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7320 (mtm110) REVERT: A 29 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7233 (ttpt) REVERT: A 195 HIS cc_start: 0.8053 (m-70) cc_final: 0.7200 (t-170) REVERT: A 273 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7613 (mm) REVERT: B 221 THR cc_start: 0.8911 (t) cc_final: 0.8587 (m) REVERT: B 268 ASN cc_start: 0.7995 (t0) cc_final: 0.7703 (t0) REVERT: H 23 SER cc_start: 0.8067 (m) cc_final: 0.7817 (t) REVERT: H 90 ASP cc_start: 0.7924 (m-30) cc_final: 0.7698 (m-30) REVERT: H 221 GLU cc_start: 0.7681 (pm20) cc_final: 0.7473 (pt0) REVERT: R 109 ASN cc_start: 0.4247 (p0) cc_final: 0.3867 (m-40) REVERT: R 112 MET cc_start: 0.5636 (pmm) cc_final: 0.5365 (pmm) REVERT: R 183 THR cc_start: 0.6336 (p) cc_final: 0.6129 (t) REVERT: R 198 THR cc_start: 0.8203 (t) cc_final: 0.7985 (m) REVERT: R 202 ILE cc_start: 0.7916 (mm) cc_final: 0.7699 (mt) REVERT: R 261 VAL cc_start: 0.6845 (m) cc_final: 0.6612 (p) REVERT: R 280 TYR cc_start: 0.6702 (t80) cc_final: 0.6462 (t80) REVERT: R 393 LEU cc_start: 0.0061 (OUTLIER) cc_final: -0.0328 (pp) outliers start: 31 outliers final: 16 residues processed: 181 average time/residue: 0.2093 time to fit residues: 51.9702 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109988 restraints weight = 11288.801| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.96 r_work: 0.3092 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8986 Z= 0.164 Angle : 0.574 9.420 12195 Z= 0.298 Chirality : 0.043 0.155 1405 Planarity : 0.004 0.044 1532 Dihedral : 4.137 35.669 1231 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 3.41 % Allowed : 12.79 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1119 helix: 2.40 (0.27), residues: 384 sheet: 1.32 (0.32), residues: 259 loop : -1.21 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 PHE 0.012 0.002 PHE H 178 TYR 0.014 0.002 TYR R 275 ARG 0.006 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 433) hydrogen bonds : angle 4.28586 ( 1203) SS BOND : bond 0.01121 ( 3) SS BOND : angle 2.65392 ( 6) covalent geometry : bond 0.00380 ( 8983) covalent geometry : angle 0.57072 (12189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7477 (mtm110) REVERT: A 29 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7258 (ttpt) REVERT: A 195 HIS cc_start: 0.8103 (m-70) cc_final: 0.7097 (t-170) REVERT: A 249 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 252 SER cc_start: 0.8940 (t) cc_final: 0.8642 (m) REVERT: A 273 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7508 (mm) REVERT: A 305 CYS cc_start: 0.8039 (t) cc_final: 0.7349 (m) REVERT: B 146 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 221 THR cc_start: 0.8903 (t) cc_final: 0.8594 (m) REVERT: B 243 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 268 ASN cc_start: 0.7950 (t0) cc_final: 0.7719 (t0) REVERT: G 15 LEU cc_start: 0.7879 (tt) cc_final: 0.7621 (tp) REVERT: H 90 ASP cc_start: 0.8450 (m-30) cc_final: 0.8203 (m-30) REVERT: H 193 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8014 (ttp) REVERT: R 112 MET cc_start: 0.5405 (pmm) cc_final: 0.5105 (pmm) REVERT: R 132 PHE cc_start: 0.7364 (t80) cc_final: 0.6754 (t80) REVERT: R 280 TYR cc_start: 0.6822 (t80) cc_final: 0.6618 (t80) REVERT: R 303 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.6714 (tpt170) outliers start: 32 outliers final: 18 residues processed: 165 average time/residue: 0.2201 time to fit residues: 49.2206 Evaluate side-chains 155 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 255 ASN H 187 GLN R 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112286 restraints weight = 11123.939| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.89 r_work: 0.3127 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8986 Z= 0.115 Angle : 0.507 6.188 12195 Z= 0.265 Chirality : 0.041 0.148 1405 Planarity : 0.003 0.045 1532 Dihedral : 3.812 16.845 1229 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 3.52 % Allowed : 13.86 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1119 helix: 2.45 (0.27), residues: 386 sheet: 1.21 (0.32), residues: 259 loop : -1.21 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE A 196 TYR 0.013 0.001 TYR H 191 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 433) hydrogen bonds : angle 4.11232 ( 1203) SS BOND : bond 0.00843 ( 3) SS BOND : angle 2.07325 ( 6) covalent geometry : bond 0.00256 ( 8983) covalent geometry : angle 0.50529 (12189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.934 Fit side-chains REVERT: A 24 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7477 (mtm110) REVERT: A 29 LYS cc_start: 0.7592 (ttmm) cc_final: 0.7250 (ttpt) REVERT: A 186 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 195 HIS cc_start: 0.8120 (m-70) cc_final: 0.7113 (t-170) REVERT: A 249 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8460 (tt) REVERT: A 252 SER cc_start: 0.8928 (t) cc_final: 0.8645 (m) REVERT: A 273 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7591 (mm) REVERT: A 276 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6685 (tt0) REVERT: A 305 CYS cc_start: 0.8011 (t) cc_final: 0.7319 (m) REVERT: B 136 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8752 (p) REVERT: B 146 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7831 (mp) REVERT: B 221 THR cc_start: 0.8831 (t) cc_final: 0.8540 (m) REVERT: G 42 GLU cc_start: 0.8109 (tt0) cc_final: 0.7887 (tt0) REVERT: H 23 SER cc_start: 0.8260 (m) cc_final: 0.7988 (t) REVERT: R 132 PHE cc_start: 0.7379 (t80) cc_final: 0.6552 (t80) REVERT: R 185 CYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5583 (t) REVERT: R 198 THR cc_start: 0.8354 (t) cc_final: 0.8009 (t) REVERT: R 303 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.6796 (tpt170) outliers start: 33 outliers final: 17 residues processed: 166 average time/residue: 0.2245 time to fit residues: 50.9368 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107611 restraints weight = 11124.150| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.91 r_work: 0.3056 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8986 Z= 0.161 Angle : 0.552 7.677 12195 Z= 0.290 Chirality : 0.043 0.195 1405 Planarity : 0.004 0.044 1532 Dihedral : 4.054 18.519 1229 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 3.41 % Allowed : 14.82 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1119 helix: 2.40 (0.27), residues: 384 sheet: 1.05 (0.32), residues: 254 loop : -1.31 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS R 170 PHE 0.011 0.001 PHE B 234 TYR 0.013 0.001 TYR H 191 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 433) hydrogen bonds : angle 4.23774 ( 1203) SS BOND : bond 0.01134 ( 3) SS BOND : angle 2.33187 ( 6) covalent geometry : bond 0.00376 ( 8983) covalent geometry : angle 0.54933 (12189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.932 Fit side-chains REVERT: A 21 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7726 (ttm170) REVERT: A 24 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7534 (mtm110) REVERT: A 29 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7344 (ttpt) REVERT: A 195 HIS cc_start: 0.8175 (m-70) cc_final: 0.7196 (t-90) REVERT: A 249 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8480 (tt) REVERT: A 252 SER cc_start: 0.8959 (t) cc_final: 0.8675 (m) REVERT: A 273 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 276 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6675 (tt0) REVERT: A 305 CYS cc_start: 0.8106 (t) cc_final: 0.7379 (m) REVERT: B 46 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7912 (mtm-85) REVERT: B 136 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8767 (p) REVERT: B 221 THR cc_start: 0.8872 (t) cc_final: 0.8580 (m) REVERT: B 243 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (t) REVERT: G 15 LEU cc_start: 0.7966 (tt) cc_final: 0.7687 (tp) REVERT: H 23 SER cc_start: 0.8370 (m) cc_final: 0.8100 (t) REVERT: H 38 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.8201 (ttm170) REVERT: L 14 ARG cc_start: 0.6217 (ptt90) cc_final: 0.5568 (ptt-90) REVERT: R 127 ASN cc_start: 0.6780 (m-40) cc_final: 0.6334 (m110) REVERT: R 132 PHE cc_start: 0.7395 (t80) cc_final: 0.6706 (t80) REVERT: R 185 CYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5701 (t) REVERT: R 187 LEU cc_start: 0.6967 (tt) cc_final: 0.6519 (mt) REVERT: R 303 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.6622 (tpt170) outliers start: 32 outliers final: 22 residues processed: 159 average time/residue: 0.2416 time to fit residues: 51.2090 Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain H residue 221 GLU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110933 restraints weight = 11078.701| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.92 r_work: 0.3104 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8986 Z= 0.107 Angle : 0.499 6.308 12195 Z= 0.263 Chirality : 0.041 0.193 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.806 17.375 1229 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.09 % Allowed : 15.57 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1119 helix: 2.46 (0.27), residues: 386 sheet: 1.04 (0.32), residues: 259 loop : -1.26 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.011 0.001 PHE R 223 TYR 0.013 0.001 TYR H 191 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 433) hydrogen bonds : angle 4.01596 ( 1203) SS BOND : bond 0.00686 ( 3) SS BOND : angle 1.75379 ( 6) covalent geometry : bond 0.00236 ( 8983) covalent geometry : angle 0.49810 (12189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7534 (mtm110) REVERT: A 29 LYS cc_start: 0.7624 (ttmm) cc_final: 0.7260 (ttpt) REVERT: A 195 HIS cc_start: 0.8141 (m-70) cc_final: 0.7176 (t-90) REVERT: A 249 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 252 SER cc_start: 0.8934 (t) cc_final: 0.8636 (m) REVERT: A 273 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 276 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6709 (tt0) REVERT: A 305 CYS cc_start: 0.8095 (t) cc_final: 0.7365 (m) REVERT: B 46 ARG cc_start: 0.8215 (mpt180) cc_final: 0.7897 (mtm-85) REVERT: B 221 THR cc_start: 0.8797 (t) cc_final: 0.8523 (m) REVERT: B 243 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (t) REVERT: H 7 SER cc_start: 0.8794 (p) cc_final: 0.8533 (t) REVERT: H 23 SER cc_start: 0.8349 (m) cc_final: 0.8098 (t) REVERT: H 38 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8088 (ttm170) REVERT: L 14 ARG cc_start: 0.6078 (ptt90) cc_final: 0.5489 (ptt-90) REVERT: R 127 ASN cc_start: 0.6585 (m-40) cc_final: 0.6219 (m110) REVERT: R 170 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.6258 (p90) REVERT: R 185 CYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5534 (t) REVERT: R 187 LEU cc_start: 0.6913 (tt) cc_final: 0.6474 (mt) REVERT: R 198 THR cc_start: 0.8363 (t) cc_final: 0.7993 (t) REVERT: R 303 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.6560 (tpt170) outliers start: 29 outliers final: 18 residues processed: 154 average time/residue: 0.2333 time to fit residues: 48.0056 Evaluate side-chains 149 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 170 HIS Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109168 restraints weight = 11204.348| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8986 Z= 0.131 Angle : 0.522 6.858 12195 Z= 0.274 Chirality : 0.042 0.199 1405 Planarity : 0.003 0.043 1532 Dihedral : 3.876 17.653 1229 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 4.05 % Allowed : 14.82 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1119 helix: 2.45 (0.27), residues: 385 sheet: 0.88 (0.32), residues: 266 loop : -1.23 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS R 170 PHE 0.010 0.001 PHE A 196 TYR 0.012 0.001 TYR H 191 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 433) hydrogen bonds : angle 4.05743 ( 1203) SS BOND : bond 0.00936 ( 3) SS BOND : angle 2.00768 ( 6) covalent geometry : bond 0.00302 ( 8983) covalent geometry : angle 0.52066 (12189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.920 Fit side-chains REVERT: A 21 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7917 (ttp-110) REVERT: A 24 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7609 (mtm110) REVERT: A 29 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7268 (ttpt) REVERT: A 195 HIS cc_start: 0.8159 (m-70) cc_final: 0.7160 (t-170) REVERT: A 198 MET cc_start: 0.8825 (ttm) cc_final: 0.8520 (mtm) REVERT: A 249 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 252 SER cc_start: 0.8935 (t) cc_final: 0.8614 (m) REVERT: A 273 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7619 (mm) REVERT: A 276 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6742 (tt0) REVERT: A 305 CYS cc_start: 0.8072 (t) cc_final: 0.7347 (m) REVERT: B 46 ARG cc_start: 0.8278 (mpt180) cc_final: 0.7950 (mtm-85) REVERT: B 136 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8776 (p) REVERT: B 221 THR cc_start: 0.8849 (t) cc_final: 0.8563 (m) REVERT: B 243 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8348 (t) REVERT: H 7 SER cc_start: 0.8805 (p) cc_final: 0.8525 (t) REVERT: H 23 SER cc_start: 0.8356 (m) cc_final: 0.8105 (t) REVERT: H 38 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.8127 (ttm170) REVERT: H 167 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8939 (tt) REVERT: R 185 CYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5561 (t) REVERT: R 187 LEU cc_start: 0.6900 (tt) cc_final: 0.6449 (mt) REVERT: R 198 THR cc_start: 0.8436 (t) cc_final: 0.8063 (t) REVERT: R 303 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.6517 (tpt170) outliers start: 38 outliers final: 24 residues processed: 152 average time/residue: 0.2493 time to fit residues: 50.0616 Evaluate side-chains 156 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108187 restraints weight = 11311.049| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.06 r_work: 0.3049 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8986 Z= 0.147 Angle : 0.540 7.176 12195 Z= 0.284 Chirality : 0.042 0.200 1405 Planarity : 0.004 0.045 1532 Dihedral : 3.994 17.869 1229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.73 % Allowed : 15.14 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1119 helix: 2.39 (0.27), residues: 384 sheet: 0.83 (0.32), residues: 265 loop : -1.26 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 170 PHE 0.010 0.001 PHE H 27 TYR 0.011 0.001 TYR R 342 ARG 0.007 0.000 ARG R 325 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 433) hydrogen bonds : angle 4.12566 ( 1203) SS BOND : bond 0.00981 ( 3) SS BOND : angle 2.04572 ( 6) covalent geometry : bond 0.00340 ( 8983) covalent geometry : angle 0.53797 (12189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 2.305 Fit side-chains REVERT: A 21 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7756 (ttm170) REVERT: A 29 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7305 (ttpt) REVERT: A 195 HIS cc_start: 0.8154 (m-70) cc_final: 0.7158 (t-170) REVERT: A 198 MET cc_start: 0.8836 (ttm) cc_final: 0.8516 (mtm) REVERT: A 249 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8413 (tt) REVERT: A 252 SER cc_start: 0.8911 (t) cc_final: 0.8608 (m) REVERT: A 273 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7621 (mm) REVERT: A 276 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6731 (tt0) REVERT: A 280 LYS cc_start: 0.7386 (pttt) cc_final: 0.7014 (pptt) REVERT: A 305 CYS cc_start: 0.8065 (t) cc_final: 0.7388 (m) REVERT: B 6 GLN cc_start: 0.7598 (tt0) cc_final: 0.7395 (tt0) REVERT: B 46 ARG cc_start: 0.8272 (mpt180) cc_final: 0.7955 (mtm-85) REVERT: B 221 THR cc_start: 0.8838 (t) cc_final: 0.8563 (m) REVERT: B 243 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8403 (t) REVERT: H 7 SER cc_start: 0.8813 (p) cc_final: 0.8557 (t) REVERT: H 23 SER cc_start: 0.8320 (m) cc_final: 0.8058 (t) REVERT: H 38 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8187 (ttm170) REVERT: H 167 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8965 (tt) REVERT: R 185 CYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5652 (t) REVERT: R 187 LEU cc_start: 0.6858 (tt) cc_final: 0.6435 (mt) REVERT: R 303 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.6524 (tpt170) outliers start: 35 outliers final: 26 residues processed: 153 average time/residue: 0.2614 time to fit residues: 53.7477 Evaluate side-chains 152 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS H 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105704 restraints weight = 11261.494| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.06 r_work: 0.3007 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8986 Z= 0.187 Angle : 0.586 8.608 12195 Z= 0.308 Chirality : 0.044 0.213 1405 Planarity : 0.004 0.043 1532 Dihedral : 4.249 20.187 1229 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 3.94 % Allowed : 15.14 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1119 helix: 2.27 (0.27), residues: 383 sheet: 0.66 (0.32), residues: 266 loop : -1.40 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS R 170 PHE 0.013 0.002 PHE B 234 TYR 0.012 0.001 TYR R 342 ARG 0.006 0.001 ARG R 325 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 433) hydrogen bonds : angle 4.31587 ( 1203) SS BOND : bond 0.01308 ( 3) SS BOND : angle 2.51131 ( 6) covalent geometry : bond 0.00439 ( 8983) covalent geometry : angle 0.58309 (12189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.039 Fit side-chains REVERT: A 21 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7804 (ttm170) REVERT: A 29 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7391 (ttpt) REVERT: A 195 HIS cc_start: 0.8170 (m-70) cc_final: 0.7152 (t-170) REVERT: A 198 MET cc_start: 0.8858 (ttm) cc_final: 0.8560 (mtm) REVERT: A 249 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 252 SER cc_start: 0.8949 (t) cc_final: 0.8652 (m) REVERT: A 273 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (mm) REVERT: A 280 LYS cc_start: 0.7241 (pttt) cc_final: 0.6903 (pptt) REVERT: A 305 CYS cc_start: 0.8097 (t) cc_final: 0.7385 (m) REVERT: B 6 GLN cc_start: 0.7623 (tt0) cc_final: 0.7413 (tt0) REVERT: B 46 ARG cc_start: 0.8267 (mpt180) cc_final: 0.7964 (mtm-85) REVERT: B 136 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8784 (p) REVERT: B 221 THR cc_start: 0.8893 (t) cc_final: 0.8616 (m) REVERT: H 7 SER cc_start: 0.8786 (p) cc_final: 0.8554 (t) REVERT: H 23 SER cc_start: 0.8362 (m) cc_final: 0.8097 (t) REVERT: H 38 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.8330 (ttm170) REVERT: R 185 CYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5783 (t) REVERT: R 187 LEU cc_start: 0.6986 (tt) cc_final: 0.6452 (mt) REVERT: R 198 THR cc_start: 0.8442 (t) cc_final: 0.8102 (t) REVERT: R 279 LEU cc_start: 0.6841 (mm) cc_final: 0.6585 (mt) REVERT: R 303 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.6485 (tpt170) outliers start: 37 outliers final: 27 residues processed: 150 average time/residue: 0.2292 time to fit residues: 46.5288 Evaluate side-chains 153 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 375 LEU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0020 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 chunk 47 optimal weight: 0.7980 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS H 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109653 restraints weight = 11174.293| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.97 r_work: 0.3083 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8986 Z= 0.108 Angle : 0.516 6.492 12195 Z= 0.270 Chirality : 0.041 0.204 1405 Planarity : 0.003 0.050 1532 Dihedral : 3.912 18.755 1229 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 2.56 % Allowed : 16.20 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1119 helix: 2.39 (0.27), residues: 385 sheet: 0.75 (0.32), residues: 266 loop : -1.34 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 170 PHE 0.009 0.001 PHE R 223 TYR 0.014 0.001 TYR H 191 ARG 0.006 0.000 ARG R 325 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 433) hydrogen bonds : angle 4.05844 ( 1203) SS BOND : bond 0.00621 ( 3) SS BOND : angle 2.62331 ( 6) covalent geometry : bond 0.00233 ( 8983) covalent geometry : angle 0.51296 (12189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7971 (ttp-110) REVERT: A 29 LYS cc_start: 0.7611 (ttmm) cc_final: 0.7238 (ttpt) REVERT: A 195 HIS cc_start: 0.8167 (m-70) cc_final: 0.7153 (t-170) REVERT: A 198 MET cc_start: 0.8793 (ttm) cc_final: 0.8492 (mtm) REVERT: A 249 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 252 SER cc_start: 0.8972 (t) cc_final: 0.8659 (m) REVERT: A 273 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7600 (mm) REVERT: A 280 LYS cc_start: 0.7300 (pttt) cc_final: 0.6946 (pptt) REVERT: A 305 CYS cc_start: 0.8058 (t) cc_final: 0.7370 (m) REVERT: B 146 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 221 THR cc_start: 0.8808 (t) cc_final: 0.8564 (m) REVERT: B 243 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (t) REVERT: H 7 SER cc_start: 0.8801 (p) cc_final: 0.8547 (t) REVERT: H 23 SER cc_start: 0.8391 (m) cc_final: 0.8148 (t) REVERT: H 38 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8208 (ttm170) REVERT: R 185 CYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5657 (t) REVERT: R 187 LEU cc_start: 0.6899 (tt) cc_final: 0.6417 (mt) REVERT: R 198 THR cc_start: 0.8401 (t) cc_final: 0.8061 (t) REVERT: R 279 LEU cc_start: 0.6771 (mm) cc_final: 0.6495 (mt) REVERT: R 303 ARG cc_start: 0.7503 (mmm-85) cc_final: 0.6538 (tpt170) outliers start: 24 outliers final: 19 residues processed: 149 average time/residue: 0.2472 time to fit residues: 49.0620 Evaluate side-chains 148 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 374 CYS Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain R residue 393 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108755 restraints weight = 11240.906| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.92 r_work: 0.3067 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.126 Angle : 0.532 6.531 12195 Z= 0.279 Chirality : 0.041 0.212 1405 Planarity : 0.004 0.045 1532 Dihedral : 3.918 18.332 1229 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 2.88 % Allowed : 15.99 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1119 helix: 2.40 (0.27), residues: 383 sheet: 0.72 (0.32), residues: 266 loop : -1.32 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE H 27 TYR 0.012 0.001 TYR H 191 ARG 0.006 0.000 ARG R 325 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 433) hydrogen bonds : angle 4.07757 ( 1203) SS BOND : bond 0.00904 ( 3) SS BOND : angle 2.88103 ( 6) covalent geometry : bond 0.00287 ( 8983) covalent geometry : angle 0.52870 (12189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5377.09 seconds wall clock time: 93 minutes 35.89 seconds (5615.89 seconds total)